Here are my options on how it is going to end:
1) Haibara and Conan were able to defeat BO and got the antidote for APTX4869. After that, they don't have to hide their identities anymore. Shinichi goes back to Teitan HS. As for Haibara, she took the antidote and had gone to Teitan HS with Shinichi too. Meeting new friends, solving new cases, and what not.
2) After defeating BO, everyone died.
3) They defeated BO and got the antidote. Shinichi goes back to Teitan HS but Haibara stays as Haibara Ai.
4) After defeating BO, there were some remains of the org, so haibara and conan thought it would be dangerous for everyone to celebrate the comeback of shinichi and shiho, so they remain kids.
5) one of haibara's relatives help them on their way of defeating BO, this hasn't been finished, it would be either they defeat BO or not, or they would find a cure but not use it.
If you have any more suggestions, feel free to post here. Any agreements or negative comments? Just post here.

